{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Given a cyclic peptide Peptide and a spectrum Spectrum, we define Score(Peptide, Spectrum) as the number of masses shared between Cyclospectrum(Peptide) and Spectrum."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "aminoacidMass = {'G':57, 'A':71, 'S':87, 'P':97, 'V':99, 'T':101, 'C':103, 'I':113, 'L':113, 'N':114, 'D':115, 'K':128, 'Q':128, 'E':129, 'M':131, 'H':137, 'F':147, 'R':156, 'Y':163, 'W':186}\n",
    "def cyclicSpectrum(peptide):\n",
    "    \"\"\"Input: An amino acid string Peptide.\n",
    "     Output: The cyclic spectrum of Peptide.\"\"\"\n",
    "    prefixMass = [0]*((len(peptide)+1))\n",
    "    for i in range(len(peptide)):\n",
    "        prefixMass[i+1] = prefixMass[i] + aminoacidMass[peptide[i]]\n",
    "    peptideMass = prefixMass[len(peptide)]\n",
    "    cyclic_spectrum = [0]\n",
    "    for i in range(len(prefixMass)-1):\n",
    "        for j in range(i+1, len(prefixMass)):\n",
    "            cyclic_spectrum.append(prefixMass[j] - prefixMass[i])\n",
    "            if i > 0 and j < (len(prefixMass)-1):\n",
    "                cyclic_spectrum.append(peptideMass - (prefixMass[j] - prefixMass[i]))\n",
    "    return sorted(cyclic_spectrum) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[0, 57, 71, 71, 97, 97, 97, 99, 99, 101, 101, 101, 101, 103, 113, 113, 113, 113, 113, 115, 115, 115, 115, 128, 128, 128, 129, 129, 131, 131, 137, 156, 156, 156, 163, 163, 163, 172, 184, 186, 186, 188, 199, 204, 210, 210, 212, 212, 212, 213, 214, 214, 214, 214, 226, 227, 228, 228, 230, 231, 232, 241, 244, 257, 259, 260, 262, 281, 284, 285, 287, 289, 292, 292, 293, 293, 301, 301, 302, 311, 312, 314, 325, 325, 326, 327, 327, 327, 327, 328, 332, 341, 341, 343, 344, 356, 358, 360, 364, 373, 389, 391, 393, 394, 397, 398, 398, 400, 402, 403, 407, 409, 415, 418, 424, 425, 426, 428, 429, 440, 440, 441, 444, 445, 445, 449, 453, 454, 455, 456, 465, 472, 475, 488, 497, 499, 501, 502, 504, 504, 506, 511, 512, 512, 516, 520, 521, 526, 529, 533, 537, 539, 541, 544, 550, 554, 554, 554, 556, 559, 560, 568, 569, 569, 572, 573, 573, 578, 585, 590, 601, 609, 612, 612, 613, 617, 619, 621, 621, 625, 630, 631, 632, 638, 639, 652, 653, 653, 655, 657, 659, 666, 669, 672, 675, 684, 685, 686, 688, 689, 691, 692, 696, 697, 700, 701, 707, 709, 714, 716, 722, 724, 724, 725, 732, 734, 740, 746, 753, 756, 759, 761, 768, 768, 769, 770, 776, 781, 781, 784, 785, 792, 793, 797, 801, 804, 809, 813, 816, 818, 822, 824, 825, 829, 829, 835, 838, 845, 847, 852, 852, 853, 853, 855, 860, 865, 869, 870, 871, 872, 874, 898, 899, 900, 905, 905, 906, 910, 912, 912, 913, 919, 919, 923, 924, 932, 938, 939, 942, 948, 948, 953, 954, 956, 957, 965, 966, 970, 973, 974, 980, 981, 984, 985, 987, 987, 999, 1002, 1010, 1013, 1013, 1016, 1016, 1020, 1024, 1027, 1028, 1032, 1036, 1041, 1049, 1051, 1055, 1061, 1061, 1062, 1066, 1067, 1069, 1070, 1073, 1082, 1083, 1084, 1085, 1086, 1087, 1097, 1098, 1102, 1102, 1113, 1114, 1117, 1117, 1131, 1133, 1133, 1137, 1137, 1137, 1138, 1141, 1141, 1142, 1144, 1152, 1158, 1162, 1166, 1170, 1176, 1179, 1186, 1186, 1195, 1196, 1198, 1198, 1199, 1199, 1201, 1204, 1211, 1213, 1213, 1213, 1215, 1225, 1226, 1232, 1234, 1243, 1244, 1246, 1250, 1250, 1259, 1265, 1265, 1269, 1269, 1273, 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4459, 4461, 4461, 4462, 4462, 4462, 4475, 4475, 4475, 4475, 4477, 4477, 4477, 4477, 4477, 4487, 4489, 4489, 4489, 4489, 4491, 4491, 4493, 4493, 4493, 4519, 4519, 4533, 4590]\n"
     ]
    }
   ],
   "source": [
    "print cyclicSpectrum('VYYEVDWTMGRQIDPDEYPIAQCTRHRATILTLPDWQM')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "aminoacidMass = {'G':57, 'A':71, 'S':87, 'P':97, 'V':99, 'T':101, 'C':103, 'I':113, 'L':113, 'N':114, 'D':115, 'K':128, 'Q':128, 'E':129, 'M':131, 'H':137, 'F':147, 'R':156, 'Y':163, 'W':186}\n",
    "from collections import Counter\n",
    "def score_peptide(peptide, spectrum):\n",
    "    \"\"\"Cyclopeptide Scoring Problem: Compute the score of a cyclic peptide against a spectrum.\n",
    "     Input: An amino acid string Peptide and a collection of integers Spectrum. \n",
    "     Output: The score of Peptide against Spectrum, Score(Peptide, Spectrum).\"\"\"\n",
    "    spectrum_peptide = cyclicSpectrum(peptide)\n",
    "    c1, c2 = Counter(spectrum_peptide), Counter(spectrum)\n",
    "    return sum([min(n, c2[k]) for k,n in c1.items()])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "8"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "score_peptide('MAMA', [0, 71, 178, 202, 202, 202, 333, 333, 333, 404, 507, 507])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "11"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "peptide = 'NKEL'\n",
    "spectrum = [0, 99, 113, 114, 128, 227, 257, 299, 355, 356, 370, 371, 484]\n",
    "score_peptide(peptide, spectrum)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "peptide VYYEVDWTMGRQIDPDEYPIAQCTRHRATILTLPDWQM\n",
      "spectrum [0, 71, 71, 87, 87, 97, 97, 99, 101, 101, 101, 101, 103, 113, 113, 113, 113, 113, 115, 115, 115, 115, 128, 128, 129, 129, 131, 131, 137, 147, 156, 156, 156, 163, 163, 163, 163, 172, 184, 186, 186, 199, 204, 210, 212, 212, 214, 214, 214, 216, 218, 226, 227, 228, 230, 231, 232, 243, 244, 244, 257, 259, 260, 260, 262, 273, 276, 278, 278, 281, 285, 287, 292, 293, 293, 301, 302, 303, 312, 314, 319, 325, 326, 327, 327, 327, 327, 328, 331, 332, 341, 358, 360, 364, 373, 374, 374, 375, 377, 389, 390, 391, 393, 394, 398, 402, 403, 407, 407, 409, 415, 416, 418, 425, 428, 429, 440, 440, 441, 441, 444, 445, 449, 456, 464, 465, 472, 475, 488, 490, 492, 494, 497, 499, 502, 503, 503, 504, 504, 505, 505, 512, 516, 517, 520, 521, 521, 531, 540, 541, 544, 550, 554, 556, 559, 560, 569, 570, 572, 573, 577, 578, 587, 592, 592, 601, 603, 605, 612, 613, 617, 618, 618, 619, 621, 621, 622, 625, 628, 634, 634, 653, 655, 657, 659, 661, 669, 671, 672, 675, 678, 680, 684, 688, 691, 696, 701, 704, 705, 707, 714, 715, 716, 716, 718, 721, 722, 723, 724, 732, 734, 735, 743, 748, 749, 749, 756, 768, 769, 775, 776, 781, 781, 785, 791, 792, 799, 800, 804, 806, 808, 809, 816, 819, 822, 822, 825, 829, 829, 830, 835, 836, 836, 843, 846, 847, 850, 852, 852, 870, 872, 877, 879, 887, 890, 895, 900, 904, 905, 905, 906, 912, 913, 919, 919, 921, 923, 928, 931, 932, 935, 937, 938, 942, 942, 944, 947, 948, 948, 953, 959, 961, 965, 976, 985, 985, 985, 992, 999, 1005, 1008, 1013, 1015, 1016, 1020, 1024, 1024, 1028, 1032, 1035, 1036, 1036, 1036, 1043, 1046, 1049, 1050, 1051, 1061, 1061, 1062, 1062, 1066, 1068, 1069, 1073, 1075, 1076, 1089, 1090, 1098, 1100, 1114, 1117, 1122, 1123, 1131, 1132, 1133, 1133, 1133, 1137, 1137, 1137, 1139, 1141, 1148, 1149, 1152, 1155, 1160, 1162, 1162, 1163, 1174, 1174, 1176, 1179, 1183, 1191, 1198, 1199, 1201, 1201, 1204, 1219, 1220, 1224, 1225, 1229, 1232, 1232, 1234, 1244, 1245, 1248, 1250, 1250, 1252, 1252, 1253, 1261, 1261, 1262, 1263, 1264, 1265, 1273, 1280, 1288, 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     ]
    }
   ],
   "source": [
    "#Reading the data\n",
    "with open('input/CyclicScoring.txt') as f:\n",
    "    peptide, spectrum = [line.strip() if i==0 else map(int,line.strip().split()) for i, line in enumerate(f.readlines())]\n",
    "print 'peptide', peptide\n",
    "print 'spectrum', spectrum"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Final code for Cyclopeptide Scoring Problem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "759"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "aminoacidMass = {'G':57, 'A':71, 'S':87, 'P':97, 'V':99, 'T':101, 'C':103, 'I':113, 'L':113, 'N':114, 'D':115, 'K':128, 'Q':128, 'E':129, 'M':131, 'H':137, 'F':147, 'R':156, 'Y':163, 'W':186}\n",
    "def cyclicSpectrum(peptide):\n",
    "    \"\"\"Input: An amino acid string Peptide.\n",
    "     Output: The cyclic spectrum of Peptide.\"\"\"\n",
    "    prefixMass = [0]*((len(peptide)+1))\n",
    "    for i in range(len(peptide)):\n",
    "        prefixMass[i+1] = prefixMass[i] + aminoacidMass[peptide[i]]\n",
    "    peptideMass = prefixMass[len(peptide)]\n",
    "    cyclic_spectrum = [0]\n",
    "    for i in range(len(prefixMass)-1):\n",
    "        for j in range(i+1, len(prefixMass)):\n",
    "            cyclic_spectrum.append(prefixMass[j] - prefixMass[i])\n",
    "            if i > 0 and j < (len(prefixMass)-1):\n",
    "                cyclic_spectrum.append(peptideMass - (prefixMass[j] - prefixMass[i]))\n",
    "    return sorted(cyclic_spectrum) \n",
    "\n",
    "from collections import Counter\n",
    "def score_peptide(peptide, spectrum):\n",
    "    \"\"\"Cyclopeptide Scoring Problem: Compute the score of a cyclic peptide against a spectrum.\n",
    "     Input: An amino acid string Peptide and a collection of integers Spectrum. \n",
    "     Output: The score of Peptide against Spectrum, Score(Peptide, Spectrum).\"\"\"\n",
    "    spectrum_peptide = cyclicSpectrum(peptide)\n",
    "    c1, c2 = Counter(spectrum_peptide), Counter(spectrum)\n",
    "    return sum([min(n, c2[k]) for k,n in c1.items()])\n",
    "\n",
    "#Reading the data\n",
    "with open('input/rosalind_ba4f.txt') as f:\n",
    "    peptide, spectrum = [line.strip() if i==0 else map(int,line.strip().split()) for i, line in enumerate(f.readlines())]\n",
    "    \n",
    "#Calling the function to compute score\n",
    "score_peptide(peptide, spectrum)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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